Hopla

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Family/disease information



Important note: this is a toy example and thus contains very few data points, making the algorithms less accurate

Case: classic trio-analysis

Result: sample_A is a child with a hetero-uniparental disomy at chr1



Family tree





Filter 0: single nucleotide variants



Variant statistics

Number of variants table

Allelic drop-out (ADO) & allelic drop-in (ADI)

sample_C

no two parents provided

sample_B

no two parents provided

sample_A

ADO = 15.16%

ADI = 0.22%

Variant depth

Number of variants profile

Vcf-based copy number (bam-based verification recommended)



Filter 1: filter 0, –dp.hard.limit, –af.hard.limit and –dp.soft.limit



Variant statistics

Number of variants table

Allelic drop-out (ADO) & allelic drop-in (ADI)

sample_C

no two parents provided

sample_B

no two parents provided

sample_A

ADO = 12.92%

ADI = 0.06%

Variant depth

Number of variants profile

B-allele frequency (BAF), region(s) of interest

chr1:40,707,070:100,808,080

B-allele frequency (BAF), genome-wide

sample_A (A)

Mendelian errors

Parent mapping

sample_A (A)



Filter 2: filter 0, filter 1, –keep.informative.ids and –keep.hetero.ids



Variant statistics

Number of variants table

Variant depth

Number of variants profile